Locus 2041

Sequence ID	2L_DroMel_CAF1
Location	5,512,268 – 5,512,364
Length	96
Max. P	0.874322

overview

Window 5

Location	5,512,268 – 5,512,364
Length	96
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	80.53
Mean single sequence MFE	-23.52
Consensus MFE	-13.77
Energy contribution	-14.37
Covariance contribution	0.60
Combinations/Pair	1.19
Mean z-score	-1.80
Structure conservation index	0.59
SVM decision value	0.05
SVM RNA-class probability	0.558174
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5512268 96 + 22407834
GCAACAGUGACAGAGUUUUCUUUUUAAGUCACAAUCGGCGAAAGCCAAUCGCUUUGCUGCCUAAUAUUU-AUACCGUGUAAUAGAGGCAUUACU---AGA
((((..(((((((((....))))....)))))....(((....))).......))))(((((.....((-((.....))))...))))).....---... ( -24.80)
>DroSec_CAF1 135992 96 + 1
GCAACAGUGACAGAGUUUUCUUUUUAAGUCACAAUCGGCGAAAGCCAAUCGCUUUGCUGCCUAAUAUUU-AUACCGUGUAAUAGAGGCAUUACU---AGA
((((..(((((((((....))))....)))))....(((....))).......))))(((((.....((-((.....))))...))))).....---... ( -24.80)
>DroSim_CAF1 142983 96 + 1
GCAACAGUGACAGAGUUUUCUUUUUAAGUCACUAUCGGCGAAAGCCAAUCGCUUUGCUGCCUAAUAUUU-AUACCGUGCAAUAGAGGCAUUACU---AGA
((((.((((((((((....))))....))))))...(((....))).......))))(((((..(((((-((...))).)))).))))).....---... ( -23.70)
>DroWil_CAF1 195719 91 + 1
ACAGCAGCAACAAAGCUUUCUUUUUGCU------GCGGCUCAUGGCGAUUUGUUUGCUGCCUAAUAUUUUCUACCUCAU---ACAAAUAUCAAUCGUUGA
...(((((((.((((....)))))))))------))(((....(((((.....))))))))..................---.................. ( -19.60)
>DroYak_CAF1 141317 96 + 1
GCAACAGUGAAUGAGUUUUCUUUUUAAGUCGCAAUCGGCGAAAGCCAAUCGCUUUGCUGCCUAAUAUUU-AUACCGUGUAAUAGAGGCAUUGCU---AGA
((((.(((((..((.((........)).))......(((....)))..)))))))))(((((.....((-((.....))))...))))).....---... ( -24.70)
>consensus
GCAACAGUGACAGAGUUUUCUUUUUAAGUCACAAUCGGCGAAAGCCAAUCGCUUUGCUGCCUAAUAUUU_AUACCGUGUAAUAGAGGCAUUACU___AGA
((((.(((((.((((....)))).............(((....)))..)))))))))(((((......................)))))........... (-13.77 = -14.37 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	5,512,268 – 5,512,364
Length	96
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	80.53
Mean single sequence MFE	-24.61
Consensus MFE	-15.52
Energy contribution	-15.88
Covariance contribution	0.36
Combinations/Pair	1.36
Mean z-score	-2.11
Structure conservation index	0.63
SVM decision value	0.88
SVM RNA-class probability	0.874322
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5512268 96 - 22407834
UCU---AGUAAUGCCUCUAUUACACGGUAU-AAAUAUUAGGCAGCAAAGCGAUUGGCUUUCGCCGAUUGUGACUUAAAAAGAAAACUCUGUCACUGUUGC
.((---(((((((((..........)))))-...))))))((((((..(((((((((....)))))))))(((................)))..)))))) ( -26.49)
>DroSec_CAF1 135992 96 - 1
UCU---AGUAAUGCCUCUAUUACACGGUAU-AAAUAUUAGGCAGCAAAGCGAUUGGCUUUCGCCGAUUGUGACUUAAAAAGAAAACUCUGUCACUGUUGC
.((---(((((((((..........)))))-...))))))((((((..(((((((((....)))))))))(((................)))..)))))) ( -26.49)
>DroSim_CAF1 142983 96 - 1
UCU---AGUAAUGCCUCUAUUGCACGGUAU-AAAUAUUAGGCAGCAAAGCGAUUGGCUUUCGCCGAUAGUGACUUAAAAAGAAAACUCUGUCACUGUUGC
.((---(((((((((..........)))))-...))))))(((((......((((((....))))))((((((................))))))))))) ( -25.69)
>DroWil_CAF1 195719 91 - 1
UCAACGAUUGAUAUUUGU---AUGAGGUAGAAAAUAUUAGGCAGCAAACAAAUCGCCAUGAGCCGC------AGCAAAAAGAAAGCUUUGUUGCUGCUGU
.......(((((((((..---..........)))))))))((((((........((.....)).((------((((((........)))))))))))))) ( -20.20)
>DroYak_CAF1 141317 96 - 1
UCU---AGCAAUGCCUCUAUUACACGGUAU-AAAUAUUAGGCAGCAAAGCGAUUGGCUUUCGCCGAUUGCGACUUAAAAAGAAAACUCAUUCACUGUUGC
...---....(((((..........)))))-.........((((((..(((((((((....)))))))))..........(((......)))..)))))) ( -24.20)
>consensus
UCU___AGUAAUGCCUCUAUUACACGGUAU_AAAUAUUAGGCAGCAAAGCGAUUGGCUUUCGCCGAUUGUGACUUAAAAAGAAAACUCUGUCACUGUUGC
...........((((..........))))...........((((((..(((((((((....))))))))).........(((....))).....)))))) (-15.52 = -15.88 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:50 2006